Research workbench
Structure of the wnt deacylase notum from drosophila - crystal form I - 2.4A
Analyse Structure of the wnt deacylase notum from drosophila - crystal form I - 2.4A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4UZJ
- Type
- protein
- Length
- 681 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Notum
- EC
- 3.1.1.1
- UniProt
- Q9VUX3
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Notum (EC 3.1.1.1) | protein | 341 | 34% helix, 18% strand | Q9VUX3 |
| B | Notum (EC 3.1.1.1) | protein | 340 | 34% helix, 18% strand | Q9VUX3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.68 | 0.82 | 39 | empty |
| 2 | 311 | 0.67 | 0.82 | 38 | empty |
| 3 | 268 | 0.54 | 0.76 | 36 | empty |
| 4 | 243 | 0.52 | 0.76 | 37 | empty |
| 5 | 77 | 0.45 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 505 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 4UZJ · Structure of the wnt deacylase notum from drosophila - crystal form I - 2.4A · the same entry in another collection · chain A against A, TM-score 1.00
- Q9VUX3 · AlphaFold monomer V2.0 prediction for palmitoleoyl-protein carboxylesterase notum (Q9VUX3) · a predicted model of the same protein · chain B against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9VUX3
- Elsewhere: RCSB PDB 4UZJ · PDBe 4UZJ · UniProt Q9VUX3
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